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Iron in PDB 3qgk: 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)

Enzymatic activity of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)

All present enzymatic activity of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent):
3.5.1.5;

Protein crystallography data

The structure of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent), PDB code: 3qgk was solved by D.E.Tronrud, A.Robbins, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.29 / 3.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 166.980, 223.940, 395.870, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.7

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) (pdb code 3qgk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent), PDB code: 3qgk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3qgk

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Iron binding site 1 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe774

b:21.0
occ:1.00
 NE2 C:HIS273 2.1 29.2 1.0
OQ2 C:KCX218 2.2 22.4 1.0
ND1 C:HIS247 2.3 19.7 1.0
CE1 C:HIS273 3.0 29.1 1.0
CD2 C:HIS273 3.1 29.5 1.0
CX C:KCX218 3.1 22.3 1.0
FE C:FE775 3.2 31.6 1.0
CE1 C:HIS247 3.2 19.1 1.0
OQ1 C:KCX218 3.4 23.8 1.0
CG C:HIS247 3.4 18.8 1.0
O C:GLY278 3.7 35.2 1.0
NE2 C:HIS220 3.7 21.2 1.0
CB C:HIS247 3.7 15.7 1.0
CD2 C:HIS220 4.0 21.2 1.0
ND1 C:HIS273 4.2 29.8 1.0
CG C:HIS273 4.2 27.6 1.0
NE2 C:HIS135 4.3 28.7 1.0
CE1 C:HIS135 4.3 28.8 1.0
NZ C:KCX218 4.4 20.2 1.0
NE2 C:HIS247 4.4 19.6 1.0
OD1 C:ASP361 4.5 36.7 1.0
CD2 C:HIS247 4.5 19.8 1.0
OD2 C:ASP361 4.5 41.9 1.0
O C:ALA168 4.6 26.2 1.0
C C:GLY278 4.7 34.3 1.0
CE1 C:HIS220 4.8 21.1 1.0
CG C:ASP361 4.9 37.2 1.0
CA C:HIS247 4.9 14.7 1.0
CE C:KCX218 4.9 20.0 1.0

Iron binding site 2 out of 12 in 3qgk

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Iron binding site 2 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe775

b:31.6
occ:1.00
 OD1 C:ASP361 1.9 36.7 1.0
NE2 C:HIS137 2.1 26.4 1.0
NE2 C:HIS135 2.3 28.7 1.0
OQ1 C:KCX218 2.4 23.8 1.0
CE1 C:HIS137 2.9 26.3 1.0
CG C:ASP361 3.0 37.2 1.0
FE C:FE774 3.2 21.0 1.0
CE1 C:HIS135 3.2 28.8 1.0
CX C:KCX218 3.3 22.3 1.0
CD2 C:HIS137 3.4 26.6 1.0
CD2 C:HIS135 3.4 28.5 1.0
OD2 C:ASP361 3.5 41.9 1.0
OQ2 C:KCX218 3.5 22.4 1.0
O C:ALA364 4.1 63.4 1.0
O C:ALA168 4.1 26.2 1.0
ND1 C:HIS137 4.1 26.9 1.0
CB C:ASP361 4.2 33.1 1.0
NE2 C:HIS273 4.3 29.2 1.0
CG C:HIS137 4.3 25.4 1.0
ND1 C:HIS135 4.4 28.9 1.0
CG C:HIS135 4.4 26.4 1.0
CG2 C:THR170 4.5 18.6 1.0
CD2 C:HIS273 4.5 29.5 1.0
NZ C:KCX218 4.5 20.2 1.0
CA C:ASP361 4.5 31.8 1.0
CB C:ALA364 4.7 52.6 1.0
O C:ASP361 5.0 35.9 1.0

Iron binding site 3 out of 12 in 3qgk

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Iron binding site 3 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe774

b:22.4
occ:1.00
 NE2 F:HIS273 2.0 24.4 1.0
OQ2 F:KCX218 2.2 24.0 1.0
ND1 F:HIS247 2.3 26.3 1.0
CX F:KCX218 3.0 22.6 1.0
CD2 F:HIS273 3.0 24.6 1.0
CE1 F:HIS273 3.1 24.3 1.0
CE1 F:HIS247 3.1 26.4 1.0
FE F:FE775 3.1 24.5 1.0
OQ1 F:KCX218 3.1 22.8 1.0
CG F:HIS247 3.5 25.1 1.0
NE2 F:HIS220 3.6 22.3 1.0
O F:GLY278 3.9 41.8 1.0
CB F:HIS247 3.9 21.7 1.0
CD2 F:HIS220 4.0 22.4 1.0
CG F:HIS273 4.2 23.0 1.0
CE1 F:HIS135 4.2 33.3 1.0
NE2 F:HIS135 4.2 33.5 1.0
ND1 F:HIS273 4.2 25.1 1.0
NZ F:KCX218 4.3 20.9 1.0
OD2 F:ASP361 4.3 40.0 1.0
NE2 F:HIS247 4.3 26.9 1.0
OD1 F:ASP361 4.4 39.4 1.0
O F:ALA168 4.5 20.3 1.0
CD2 F:HIS247 4.5 27.0 1.0
C F:GLY278 4.6 40.9 1.0
CE1 F:HIS220 4.6 22.1 1.0
CG F:ASP361 4.7 39.0 1.0
CE F:KCX218 4.9 20.4 1.0

Iron binding site 4 out of 12 in 3qgk

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Iron binding site 4 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe775

b:24.5
occ:1.00
 OD1 F:ASP361 1.9 39.4 1.0
OQ1 F:KCX218 2.0 22.8 1.0
NE2 F:HIS135 2.2 33.5 1.0
NE2 F:HIS137 2.3 28.0 1.0
CG F:ASP361 2.9 39.0 1.0
CX F:KCX218 3.0 22.6 1.0
CE1 F:HIS135 3.1 33.3 1.0
CE1 F:HIS137 3.1 27.7 1.0
FE F:FE774 3.1 22.4 1.0
CD2 F:HIS135 3.2 33.5 1.0
CD2 F:HIS137 3.4 28.1 1.0
OD2 F:ASP361 3.4 40.0 1.0
OQ2 F:KCX218 3.5 24.0 1.0
CB F:ASP361 4.2 34.2 1.0
O F:ALA168 4.2 20.3 1.0
NZ F:KCX218 4.2 20.9 1.0
O F:ALA364 4.2 59.6 1.0
ND1 F:HIS135 4.2 33.7 1.0
CG2 F:THR170 4.3 19.9 1.0
CG F:HIS135 4.3 31.2 1.0
ND1 F:HIS137 4.3 27.8 1.0
NE2 F:HIS273 4.3 24.4 1.0
CA F:ASP361 4.4 32.6 1.0
CD2 F:HIS273 4.4 24.6 1.0
CG F:HIS137 4.5 25.9 1.0
CB F:ALA364 4.6 50.1 1.0

Iron binding site 5 out of 12 in 3qgk

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Iron binding site 5 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe774

b:24.8
occ:1.00
 NE2 I:HIS273 2.2 32.2 1.0
ND1 I:HIS247 2.2 26.3 1.0
OQ2 I:KCX218 2.4 26.1 1.0
CE1 I:HIS247 2.9 25.7 1.0
FE I:FE775 3.1 28.5 1.0
CD2 I:HIS273 3.1 32.6 1.0
CX I:KCX218 3.2 25.4 1.0
CE1 I:HIS273 3.2 32.1 1.0
OQ1 I:KCX218 3.3 27.3 1.0
CG I:HIS247 3.4 24.9 1.0
NE2 I:HIS220 3.6 24.5 1.0
O I:GLY278 3.7 43.7 1.0
CD2 I:HIS220 3.8 24.7 1.0
CB I:HIS247 3.9 21.4 1.0
NE2 I:HIS247 4.2 26.2 1.0
OD2 I:ASP361 4.2 44.7 1.0
CE1 I:HIS135 4.2 29.3 1.0
CG I:HIS273 4.3 31.1 1.0
ND1 I:HIS273 4.3 32.8 1.0
NZ I:KCX218 4.4 22.1 1.0
OD1 I:ASP361 4.4 36.1 1.0
NE2 I:HIS135 4.4 29.3 1.0
CD2 I:HIS247 4.4 26.3 1.0
O I:ALA168 4.5 27.9 1.0
C I:GLY278 4.6 42.7 1.0
CG I:ASP361 4.7 37.2 1.0
CE1 I:HIS220 4.8 24.1 1.0

Iron binding site 6 out of 12 in 3qgk

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Iron binding site 6 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe775

b:28.5
occ:1.00
 OD1 I:ASP361 2.0 36.1 1.0
NE2 I:HIS135 2.1 29.3 1.0
NE2 I:HIS137 2.2 30.4 1.0
OQ1 I:KCX218 2.2 27.3 1.0
CE1 I:HIS135 2.9 29.3 1.0
CE1 I:HIS137 3.0 30.0 1.0
CG I:ASP361 3.0 37.2 1.0
FE I:FE774 3.1 24.8 1.0
CX I:KCX218 3.2 25.4 1.0
CD2 I:HIS135 3.3 29.3 1.0
CD2 I:HIS137 3.4 30.6 1.0
OD2 I:ASP361 3.4 44.7 1.0
OQ2 I:KCX218 3.5 26.1 1.0
ND1 I:HIS135 4.1 29.8 1.0
ND1 I:HIS137 4.2 30.2 1.0
O I:ALA364 4.2 60.0 1.0
CB I:ASP361 4.3 31.6 1.0
O I:ALA168 4.3 27.9 1.0
CG I:HIS135 4.3 27.7 1.0
NZ I:KCX218 4.3 22.1 1.0
CG I:HIS137 4.4 28.2 1.0
NE2 I:HIS273 4.4 32.2 1.0
CG2 I:THR170 4.4 16.0 1.0
CD2 I:HIS273 4.5 32.6 1.0
CA I:ASP361 4.5 30.4 1.0
CB I:ALA364 4.7 51.6 1.0

Iron binding site 7 out of 12 in 3qgk

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Iron binding site 7 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe774

b:20.9
occ:1.00
 OQ2 L:KCX218 2.1 20.8 1.0
NE2 L:HIS273 2.2 31.0 1.0
ND1 L:HIS247 2.3 28.9 1.0
CX L:KCX218 3.1 20.1 1.0
FE L:FE775 3.1 30.5 1.0
CE1 L:HIS247 3.1 28.4 1.0
CD2 L:HIS273 3.2 31.2 1.0
CE1 L:HIS273 3.2 31.1 1.0
OQ1 L:KCX218 3.3 20.6 1.0
CG L:HIS247 3.4 27.2 1.0
NE2 L:HIS220 3.6 28.0 1.0
CB L:HIS247 3.7 23.4 1.0
CD2 L:HIS220 3.9 27.9 1.0
O L:GLY278 3.9 39.2 1.0
CE1 L:HIS135 4.2 31.1 1.0
OD2 L:ASP361 4.2 49.7 1.0
NZ L:KCX218 4.3 18.3 1.0
OD1 L:ASP361 4.3 42.8 1.0
CG L:HIS273 4.3 29.9 1.0
NE2 L:HIS135 4.3 31.3 1.0
NE2 L:HIS247 4.3 28.8 1.0
ND1 L:HIS273 4.4 31.7 1.0
CD2 L:HIS247 4.5 28.6 1.0
O L:ALA168 4.6 23.1 1.0
CG L:ASP361 4.7 43.5 1.0
C L:GLY278 4.7 38.0 1.0
CE1 L:HIS220 4.8 27.7 1.0
CE L:KCX218 4.8 18.4 1.0

Iron binding site 8 out of 12 in 3qgk

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Iron binding site 8 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe775

b:30.5
occ:1.00
 OD1 L:ASP361 1.7 42.8 1.0
OQ1 L:KCX218 2.2 20.6 1.0
NE2 L:HIS137 2.2 30.3 1.0
NE2 L:HIS135 2.2 31.3 1.0
CG L:ASP361 2.8 43.5 1.0
CE1 L:HIS135 3.0 31.1 1.0
CE1 L:HIS137 3.0 30.2 1.0
CX L:KCX218 3.1 20.1 1.0
FE L:FE774 3.1 20.9 1.0
OD2 L:ASP361 3.3 49.7 1.0
CD2 L:HIS137 3.3 30.8 1.0
CD2 L:HIS135 3.3 31.4 1.0
OQ2 L:KCX218 3.4 20.8 1.0
O L:ALA364 4.1 63.6 1.0
CB L:ASP361 4.1 34.2 1.0
ND1 L:HIS135 4.2 31.4 1.0
O L:ALA168 4.2 23.1 1.0
ND1 L:HIS137 4.2 31.1 1.0
NZ L:KCX218 4.3 18.3 1.0
CG L:HIS135 4.3 29.4 1.0
CG L:HIS137 4.3 29.2 1.0
CA L:ASP361 4.4 32.2 1.0
NE2 L:HIS273 4.4 31.0 1.0
CD2 L:HIS273 4.5 31.2 1.0
CB L:ALA364 4.6 53.5 1.0
CG2 L:THR170 4.7 23.5 1.0

Iron binding site 9 out of 12 in 3qgk

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Iron binding site 9 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe774

b:29.9
occ:1.00
 NE2 O:HIS273 2.1 30.6 1.0
OQ2 O:KCX218 2.2 29.7 1.0
ND1 O:HIS247 2.3 32.0 1.0
CE1 O:HIS273 3.0 30.8 1.0
CE1 O:HIS247 3.1 31.9 1.0
CD2 O:HIS273 3.1 30.7 1.0
FE O:FE775 3.2 27.4 1.0
CX O:KCX218 3.2 29.1 1.0
CG O:HIS247 3.4 30.6 1.0
O O:GLY278 3.5 37.8 1.0
OQ1 O:KCX218 3.6 28.1 1.0
NE2 O:HIS220 3.7 27.8 1.0
CB O:HIS247 3.8 27.1 1.0
CD2 O:HIS220 4.0 28.0 1.0
ND1 O:HIS273 4.2 31.6 1.0
CG O:HIS273 4.2 29.3 1.0
NE2 O:HIS135 4.3 28.8 1.0
CE1 O:HIS135 4.3 28.5 1.0
OD2 O:ASP361 4.3 47.9 1.0
NE2 O:HIS247 4.3 32.5 1.0
OD1 O:ASP361 4.4 44.8 1.0
NZ O:KCX218 4.4 29.1 1.0
CD2 O:HIS247 4.5 32.3 1.0
O O:ALA168 4.6 25.1 1.0
C O:GLY278 4.6 37.6 1.0
CG O:ASP361 4.8 44.0 1.0
CE1 O:HIS220 4.8 27.8 1.0
CE O:KCX218 4.9 28.8 1.0

Iron binding site 10 out of 12 in 3qgk

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Iron binding site 10 out of 12 in the 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 3.0 A Model of Iron Containing Urease UREA2B2 From Helicobacter Mustelae (Refined W/ No Ordered Solvent) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe775

b:27.4
occ:1.00
 OD1 O:ASP361 1.8 44.8 1.0
NE2 O:HIS135 2.2 28.8 1.0
OQ1 O:KCX218 2.3 28.1 1.0
NE2 O:HIS137 2.3 34.0 1.0
CG O:ASP361 2.9 44.0 1.0
CE1 O:HIS135 3.1 28.5 1.0
CX O:KCX218 3.1 29.1 1.0
CE1 O:HIS137 3.1 33.8 1.0
FE O:FE774 3.2 29.9 1.0
CD2 O:HIS135 3.2 28.7 1.0
OQ2 O:KCX218 3.3 29.7 1.0
OD2 O:ASP361 3.3 47.9 1.0
CD2 O:HIS137 3.4 34.3 1.0
CB O:ASP361 4.1 37.5 1.0
O O:ALA364 4.2 60.7 1.0
NE2 O:HIS273 4.2 30.6 1.0
ND1 O:HIS135 4.2 28.9 1.0
O O:ALA168 4.3 25.1 1.0
NZ O:KCX218 4.3 29.1 1.0
CG O:HIS135 4.3 26.8 1.0
ND1 O:HIS137 4.4 34.4 1.0
CD2 O:HIS273 4.4 30.7 1.0
CA O:ASP361 4.4 36.1 1.0
CG O:HIS137 4.5 32.7 1.0
CG2 O:THR170 4.5 15.2 1.0
CB O:ALA364 4.7 53.3 1.0
CD2 O:TYR272 4.9 25.2 1.0

Reference:

E.L.Carter, D.E.Tronrud, S.R.Taber, P.A.Karplus, R.P.Hausinger. Iron-Containing Urease in A Pathogenic Bacterium. Proc.Natl.Acad.Sci.Usa V. 108 13095 2011.
ISSN: ISSN 0027-8424
PubMed: 21788478
DOI: 10.1073/PNAS.1106915108
Page generated: Sun Aug 4 18:39:05 2024

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